Nucleotide mixture for improved nucleic acid amplification performance

ABSTRACT

The present invention relates to modification of amplification buffer used in amplification reactions. The modifications result in a significant improvement in results of amplification. In particular, the present invention provides methods and buffers for performing an amplification reaction utilizing a buffer comprising nucleotide triphosphates comprising treating the buffer to substitute a portion of the nucleotide triphosphates with nucleotide diphosphates.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is divisional of U.S. application Ser. No. 11/040,371,filed on Jan. 21, 2005 now U.S. Pat. No. 7,364,854, which claims thebenefit of U.S. Provisional Patent Application No. 60/538,815 filed onJan. 23, 2004, U.S. Provisional Patent Application No. 60/538,814 filedon Jan. 23, 2004, and U.S. Provisional Patent Application No. 60/538,816filed on Jan. 23, 2004.

SEQUENCE LISTING

Reference is hereby made to parent U.S. application Ser. No. 11/040,371,filed on Jan. 21, 2005 now U.S. Pat. No. 7,364,854 and the computerreadable form of the Sequence Listing submitted therein. The content ofthe computer readable form in U.S. application Ser. No. 11/040,371 ishereby incorporated by reference in its entirety. The paper copy of theSequence Listing submitted herewith is identical to the computerreadable copy filed in U.S. application Ser. No. 11/040,371.

FIELD OF THE INVENTION

The present invention relates to methods of increasing the product yieldof nucleic acid amplification reactions, with the method particularlyuseful for diagnostic assays. The present invention particularly relatesto buffers useful in nucleic acid amplification reactions.

BACKGROUND OF THE INVENTION

Nucleic acid amplification has proven useful in numerous clinicalapplications including the detection and/or diagnosis of infectiousdiseases and pathological genomic abnormalities as well as nucleic acidpolymorphisms that may not be associated with any pathological state.Nucleic acid amplification is particularly useful in circumstances wherethe quantity of the targeted nucleic acid is relatively small comparedto other nucleic acids present in a sample, where only a small amount ofthe targeted nucleic acid is available, where the detection techniquehas low sensitivity, or where more rapid detection is desirable. Forexample, infectious agents may be accurately identified by detection ofspecific characteristic nucleic acid sequences. Because a relativelysmall number of pathogenic organisms may be present in a sample, the DNAextracted from these organisms typically constitutes only a very smallfraction of the total DNA in the sample. Specific amplification of thecharacteristic DNA sequences, if present, greatly enhances thesensitivity and specificity of the detection and discriminationprocesses.

Generally, the currently known amplification schemes can be broadlygrouped into two classes based on whether the enzymatic amplificationreactions are driven by continuous cycling of the temperature betweenthe denaturation temperature, the primer annealing temperature, and theamplicon (product of enzymatic amplification of nucleic acid) synthesistemperature, or whether the temperature is kept constant throughout theenzymatic amplification process (isothermal amplification). Typicalcycling nucleic acid amplification technologies (thermocycling) arepolymerase chain reaction (PCR), and ligase chain reaction (LCR).Specific protocols for such reactions are discussed in, for example,Short Protocols in Molecular Biology, 2.sup.nd Edition, A Compendium ofMethods from Current Protocols in Molecular Biology, (Eds. Ausubel etal., John Wiley & Sons, New York, 1992) chapter 15. Reactions which areisothermal include: transcription-mediated amplification (TMA), nucleicacid sequence-based amplification (NASBA), and strand displacementamplification (SDA).

U.S. Pat. No. 4,683,195 (Mullis); U.S. Pat. No. 4,965,188 (Mullis); andU.S. Pat. No. 4,683,202 (Mullis) describe a polymerase chain reaction(PCR) utilizes DNA polymerase, complementary primer molecules andrepeated cycles of thermal reactions to exponentially replicate targetnucleic acid molecules. Isothermal target amplification methods includetranscription-based amplification methods, in which an RNA polymerasepromoter sequence is incorporated into primer extension products at anearly stage of the amplification (WO 89/01050), and further targetsequence, or target complementary sequence, is amplified bytranscription steps and digestion of an RNA strand in a DNA/RNA hybridintermediate product. See, for example, U.S. Pat. Nos. 5,169,766 and4,786,600. These methods include transcription mediated amplification(TMA), self-sustained sequence replication (3SR), Nucleic Acid SequenceBased Amplification (NASBA), and variations there of. See, for example,Guatelli et al. Proc. Natl. Acad. Sci. U.S.A. 87:1874-1878 (1990); U.S.Pat. Nos. 5,766,849 5,399,491; 5,480,784; 5,766,849; and 5,654,142(TMA); and U.S. Pat. No. 5,130,238 (Malek et al.); U.S. Pat. No.5,409,818 (Davey et al.); U.S. Pat. No. 5,654,142 (Kievits); and U.S.Pat. No. 6,312,928 (Van Gemen et al.) (nucleic acid sequence-basedamplification (NASBA) techniques). U.S. Pat. No. 5,792,607 (Backman)describes amplification methods referred to as ligase chain reactions(LCR). U.S. Pat. No. 5,744,311 (Fraiser); U.S. Pat. No. 5,648,211(Fraiser) and U.S. Pat. No. 5,631,147 (Lohman), describe isothermalamplification systems based on strand displacement amplification (SDA).Other approaches include Q.beta. replicase, strand displacement assay(SDA), transcription mediated iso CR cycling probe technology, nucleicacid sequence-based amplification (NASBA) and cascade rolling circleamplification (CRCA). Additional U.S. patent documents which describenucleic acid amplification include U.S. Pat. Nos. 4,876,187; 5,030,557;5,399,491; 5,485,184; 5,554,517; 5,437,990; 5,399,491 and 5,554,516.

While many advances have been made in the area of amplification ofnucleic acids, there is still a need to improve the product yield, toachieve improved sensitivity and thus to provide more useful assays. Thepresent invention provides methods and buffers that provide increasedamplification performance of a selected nucleic acid.

SUMMARY OF THE INVENTION

The present invention provides a method for performing an amplificationreaction utilizing a buffer comprising nucleotide triphosphatescomprising treating the buffer to substitute a portion of the nucleotidetriphosphates with nucleotide diphosphates.

The present invention additionally provides an amplification reactionutilizing a buffer comprising nucleotide triphosphates comprisingtreating the buffer, prior to adding enzyme and template to the buffer,by heating the buffer to a selected temperature for a selected period oftime, the temperature and time each sufficient to increase the ratio ofnucleotide diphosphates to nucleotide triphosphates in the buffer.

The present invention further provides a buffer for amplification ofnucleic acids with nucleotide triphosphates, comprising nucleotidetriphosphates and nucleotide diphosphates, wherein at least onenucleotide diphosphate is present in a ratio of from 10:90 to 80:20total nucleotide diphosphate:total nucleotide triphosphate.

Further, the present invention provides a buffer for amplification ofnucleic acids with nucleotide triphosphates, comprising nucleotidetriphosphates and nucleotide diphosphates, wherein at least onenucleotide diphosphate is present in a ratio of from 35:65 to 80:20total nucleotide diphosphate:total nucleotide triphosphate.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides the results of HCV amplification with RAR buffersubjected to extended incubation at 4° C. (--⋄--), 25° C. (--□--), and37° C. (--Δ--), for time lengths (days) indicated, up to 48 days. Part ARate is measured in fluorescence units.

FIG. 2 shows the results of HCV nucleic acid amplification with RARbuffer subjected to extended incubation at 55° C. & 65° C., for the timelengths indicated, up to 5 days, showing rapid increase in rates(relative to lower temperatures of incubation) of improved amplificationperformance results.

FIG. 3 provides HCV nucleic acid amplification results with RAR bufferheated to 55° C., then returned to 4° C. for 3 days, showing that thetreated buffer fully maintained the higher amplification performanceafter return to 4° C.

FIG. 4 is a table providing the results (3 sets “Reps”) of HIV nucleicacid amplification using LAR buffer subjected to incubation at either 4°C. or 37° C., each for 69 days. * indicates a spiked control differentfrom the standard dilution. “CV” is coefficient of variance.

FIG. 5 provides a graph of the dynamic range for Rates A (--♦---) and B(--▪--) (see FIG. 4) using LAR buffer stored at 37° C. for 69 days.“RFU” is relative fluorescence unit.

FIG. 6 provides the linear portion (see FIGS. 4 and 5) of the Rate A(--♦---) and Rate B (--▪--) curves of amplification of HIV nucleic acidsusing LAR buffer stored at 37° C. for 69 days.

FIG. 7. FIG. 7A shows the results of HCV amplification with RAR bufferhaving partial replacement of NTPs with NDPs, showing that suchreplacement increases rates. Specifically shown are results wherein 35%of standard amount of NTP (see Table 2) is replaced with NDP; whereinonly 65% of standard amount of NTP is used (with no NDPs); wherein 100%of the standard amounts of NTPs are used and additionally an amountequivalent to 35% of standard amount (of NTP) of NDP is added; andwherein 100% of standard amount of NTP is used and no additionalnucleotides in the form of NDP are added. FIG. 7B shows a repeatexperiment with the 65%/35% replacement. Data corresponds with Tables 6Aand 6B herein.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to modification of the amplificationbuffer for amplification reactions. The modifications result in asignificant improvement in results of amplification As stated above, thepresent invention provides a method for performing an amplificationreaction utilizing a buffer comprising nucleotide triphosphatescomprising treating the buffer to substitute a portion of the nucleotidetriphosphates with nucleotide diphosphates. The present inventionfurther provides a buffer comprising nucleotide triphosphates whereinthe buffer has been treated in a manner that results in the substitutionof a portion of the nucleotide triphosphates with nucleotidediphosphates.

As used in the specification and the claims, to “substitute” includesany means by which a portion of the nucleotide triphosphates (NTPs) arereplaced by nucleotide diphosphates (NDPs), including, for example anychemical, physical or mechanical means by which this may beaccomplished. For example, a portion of the NTPs may simply be left outof the buffer and that portion replaced by NDPs, or a portion of theNTPs may be converted to NDPs, such as by heating the buffer asdescribed herein. The portion replaced should be a portion whereinamplification is improved, e.g., wherein the level of amplification isincreased or the time of amplification necessary to have a useful resultis reduced or assay sensitivity is increased.

As used in the claims, “treatment” can include any means by which thesubstitution of a portion of the nucleotide triphosphates withnucleotide diphosphates can be accomplished without significantdetrimental effects to the end-point use of the treated buffer, e.g.,without significantly decreasing the resulting amplification. Forexample, the substitution of a portion of the nucleotide triphosphateswith nucleotide diphosphates can be accomplished by heat-treating thebuffer, as described herein. Alternatively, another example of achievingsuch substitution is by replacing, in the amplification buffer, aportion of the initial amount of NTPs with NDPs, maintaining theoriginal concentration of nucleotides (all NTPS and NDPs) in thereaction. That is, a portion of the original standard amount NTPs areleft out of the reaction and that same portion is replaced by NDPs inthe reaction. This example is also further described herein.

In a preferred embodiment, the treatment comprises, prior to addingenzyme and template to the buffer, heating the buffer to a selectedtemperature for a selected period of time, the temperature and time eachsufficient to increase the ratio of nucleotide diphosphates tonucleotide triphosphates in the buffer. “Heating” as used in the claimsmeans heating the buffer to a temperature above ambient, or room,temperature. Heating can mean placing the buffer in an appropriateheating apparatus set for the selected temperature, but ideally itincludes bringing the buffer temperature to that selected temperature.Heating temperatures can range from just above room temperature to theboiling point of the buffer, with preferable temperatures falling withinthat range. For example, a preferred temperature range is between about25° C. and about 75° C., more preferably between about 25° C. and about65° C., more preferably between about 37° C. and about 65° C. Whendescribing a temperature, in the claims, “about” typically means withintwo, and preferably one, degree of the stated temperature. The timeperiod for heating can be selected based upon the temperature selected.In general, the higher the temperature selected, the shorter thepreferred period of time, and the lower the temperature, the longer thepreferred period of time; i.e., the temperature and the time selectedfor that temperature are typically inversely related. For example, if aselected temperature is between about 37° C. and about 55° C., the timeperiod may preferably be at least about 7 days; if a selectedtemperature is above about 55° C., the time period may preferably be upto about 4 days.

As taught herein, improvements to amplification buffers can be achievedby heating a selected amplification buffer at a selected temperature fora selected period of time. Typically, the period of time, regardless ofthe temperature selected, will be at least about 12 hours, morepreferably 18 hours, and even more preferably, 24 hours. Furthermore,particularly at lower temperatures (e.g., 37° C. or lower), the periodof time can be significantly longer. For example, the period of time canbe at least about 14 days; it can be at least about 21 days; it can beat least about 30 days; it can be at least about 45 days; and it can beat least about 69 days. Given the teachings provided herein, the skilledartisan can select a temperature and incubation time optimal for aparticular amplification reaction. In particular, a skilled artisan,given the teachings herein, can select a desired ratio of NDPs to NTPsand determine the optimal temperature and incubation time for the bufferto achieve the desired ratio of NDPs to NTPs.

As used in the claims to “increase the ratio” means to increase theratio to a point wherein amplification is improved, e.g., wherein thelevel of amplification is increased, the time of amplification necessaryto have a useful result is reduced, or assay sensitivity is increased.As used in the claims “the ratio of at least one nucleotide diphosphateto total nucleotide triphosphate” is the ratio of NDPs to NTPs,regardless of whether the NDPs contributing to the buffer include one,two, three or all four NDPs (i.e., ADP, CDP, GDP and/or TDP), andregardless of what mixture of NDPs comprise the portion of NDPs. TheNDPs can be any selected combination of one, two, three or four NDPs, atany selected ratios of one NDP to any other. Based upon the teachingsprovided herein, the skilled artisan can select specific combinations ofNDPs suitable for the particular amplification reaction to be performed.Furthermore, as taught herein, heating can be used to achieve thedesired ratio of NDPs to NTPs without necessarily the need particularlyto measure which and what portion of NDPs are present in the buffer. Onecan readily determine the relative proportions of NDPs and NTPs in anyprepared buffer of the invention after treating by heat, at a selectedtemperature and for selected time period, using means such as thosedescribed herein, e.g., HPLC analysis.

A preferred embodiment is one wherein the selected temperature and timeperiod are sufficient to increase the ratio of at least one nucleotidediphosphate to total nucleotide triphosphate to a range from about 5:90to about 80:20 total nucleotide diphosphate:total nucleotidetriphosphate. More preferred is a ratio of a range of from about 10:90to about 80:20 total nucleotide diphosphate:total nucleotidetriphosphate. Yet more preferred is a ratio of a range from about 35:65to about 80:20 total nucleotide diphosphate:total nucleotidetriphosphate. As used to describe a ratio within the invention, “about”can provide for slight variations outside the recited numerical rangewherein the herein demonstrated improved function of the buffer isretained. Preferred buffers of the invention have a ratio of totalnucleotide diphosphate:total nucleotide triphosphate of 35:65, 40:60;45:55, 50:50, 55:45, 60:40, 65:35, 70:30, 75:35, and 80:20. As mentionedabove, the total nucleotide diphosphate can comprise any selectedcombinations of nucleotides, including modified nucleotides.

As taught herein, improvements to amplification buffers can comprisetreating the buffer wherein such treatment comprises replacing a portionof at least one nucleotide triphosphate in the buffer with nucleotidediphosphate. In a preferred embodiment, the portion of nucleotidetriphosphates replaced with nucleotide diphosphates is selected frombetween about 5% and 80%. As used herein “about X%” can provide forslight variations outside the stated numerical percentage wherein thebuffer retains improved functioning taught herein. Specificallypreferred buffers have replaced at least 10% of the NTPs with NDPs, andmore preferred buffers have replaced 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75% and 80% of the NTPs with NDPs. A morepreferred range is between about 10% and 80%, 15% and 80%, 15% and 70%,20% and 65%, 30% and 65%, 35% and 60%, and 35% and 50%.

The present invention additionally includes buffers for amplification ofnucleic acids. Such buffers can be made, for example, by the methodsdescribed herein. The invention particularly provides a buffer foramplification of nucleic acids with nucleotide triphosphates, comprisingnucleotide triphosphates and nucleotide diphosphates, wherein the bufferhas been treated in a manner that results in the substitution of aportion of the nucleotide triphosphates with nucleotide diphosphates. Amanner that results in the substitution of a portion of the nucleotidetriphosphates with nucleotide diphosphates can include any means bywhich a portion of the nucleotide triphosphates (NTPs) are replaced bynucleotide diphosphates, such as described herein. For example, aportion of the NTPs may simply be left out of the buffer and thatportion replaced by NDPs, or a portion of the NTPs may be converted toNDPs, such as by heating the buffer as described herein.

In particular, the invention provides a buffer for amplification ofnucleic acids with nucleotide triphosphates, comprising nucleotidetriphosphates and nucleotide diphosphates, wherein at least onenucleotide diphosphate is present in a ratio of from 10:90 to 80:20total nucleotide diphosphate:total nucleotide triphosphate. Morepreferred is a ratio of a range of from about 10:90 to about 80:20 totalnucleotide diphosphate:total nucleotide triphosphate. Yet more preferredis a ratio of a range from about 35:65 to about 80:20 total nucleotidediphosphate:total nucleotide triphosphate. Preferred buffers of theinvention have a ratio of total nucleotide diphosphate:total nucleotidetriphosphate of 35:65, 40:60; 45:55, 50:50, 55:45, 60:40, 65:35, 70:30,75:35, and 80:20. As mentioned above, the total nucleotide diphosphatecan comprise any selected combinations of nucleotides, includingmodified nucleotides.

A buffer for amplification of nucleic acids with nucleotidetriphosphates, comprising nucleotide triphosphates and nucleotidediphosphates, wherein the buffer has been treated in a manner thatresults in the substitution of a portion of the nucleotide triphosphateswith nucleotide diphosphates.

In the methods and buffers of the present invention, amplificationenzymes typically would be added after the heating step, to avoidinactivating the enzymes, though this may not be necessary for use ofthermostable enzymes. The buffers of the present invention can be storedunder standard conditions, e.g., 4° C., with standard shelf life. Thebuffer can further comprise selected ingredients for the assay to beperformed. Standard amplification buffer formulations are well known inthe art, and they can be adapted readily for any of the presentinventive buffers, following the teachings herein. For example, bufferscan include Tris, magnesium and salt. Buffers can further comprise DMSO.Buffers can further comprise glycerol. More specifically, buffers caninclude Tween, such as Tween 80, Tris, EDTA, KCl, ZnAc, MgCl, glycerol,DMSO, Na Azide, primers, and/or probes.

Additionally provided herein is a buffer for amplification of nucleicacids comprising greater than 5% Tween 80. Buffers are provided hereinthat are useful for many amplification reactions, wherein the buffercomprises greater than 5% Tween 80, more preferably greater than 8%Tween 80, greater than 10% Tween 80. A preferred buffer can have 12.5%Tween 80. A buffer can have up to 15% Tween 80. Such buffers can beparticularly useful for isothermal amplification reactions.Additionally, they can be preferable when the target of amplificationhas high secondary structure. Known buffers (e.g., for TMA, U.S. Pat.No. 5,399,491) can be modified to increase the amount of Tween 80 inaccordance with the teachings of this invention to create buffers ofthis invention. Such buffers can further comprise other ingredients; forexample the buffer can further comprise DMSO; the buffer can furthercomprise glycerol; the buffer can further comprise salt. Morespecifically, such buffers can additionally include Tris, EDTA, KCl,ZnAc, MgCl, glycerol, DMSO, Na Azide, primers, and/or probes. Aparticularly preferred buffer of the present invention would have both(1) Tween 80 present at greater than 5% and (2) substitution of aportion of the nucleotide triphosphates with nucleotide diphosphates;however, each of these characteristics provides an improvement inamplification.

Buffers typically contain all four nucleotides, adenine, guanine,thymidine and cytosine; however, for certain applications, it may bethat fewer than all four bases are desired. Furthermore, in general,modified nucleotides can be used in addition to the standard nucleotidesor in partial or full substitution thereof. Such modifiedoligonucleotides are known in the art; some examples includehydroxymethyl nucleotides, methylated nucleotides, fluorinatednucleotides, alpha this phosphate nucleotides, amine-modifiednucleotides, methoxy nucleotides, carboxymethyl nucleotides, thiolnucleotides, inosine, dihydrouridine, psuedouridine, wybutosine,queuosine, C7dGTP. Additional modified nucleotides are found in U.S.Pat. Nos. 5,405,950 and 5,633,364 (both, Mock and Lovern).

The present invention further provides a kit comprising a buffer of theinvention. Such kits can include, in addition to the buffer, one or moreadditional component, such as instructions for use of the buffer,reaction containers, and additional reagents such as amplificationenzyme(s), primers, probes, additional NTPs and/or NTPs, sterilizedwater, lysis buffer, stop buffer, and the like.

Amplification methods are well known to those of skill in the art, andsuch artisans can readily apply the teachings provided herein to aselected amplification method. The amplification can be performedutilizing any amplification method that utilizes NTPs, such as DNApolymerase-based amplification reaction or a transcription-basedamplification reaction. Amplification can be performed, for example, bythermocycling methods or isothermal methods. The present methods andbuffers are particularly useful, and preferably used in, transcriptionbased amplification methods, for example, NASBA and TMA. Transcriptionbased amplification methods often utilize single stranded RNA as theinput material, although single or double stranded DNA can likewise beused as input material. When a transcription based amplification methodis practiced on a sample with single stranded RNA (of the “plus” sense)with additional sequences on both the 3′-end and the 5′ end of thetarget sequence, a pair of oligonucleotides that is conveniently usedwith the methods can include (1) a first oligonucleotide (often referredto as a “promoter-oligonucleotide”, or “P1” primer) that is capable ofhybridizing to the 3-end of the target sequence, which oligonucleotidehas the sequence of a promoter (preferably the T7 promoter) attached toits 5′ end (the hybridizing part of this oligonucleotide has theopposite polarity as the plus RNA used as input material); and (2) asecond oligonucleotide (“primer”) which comprises the 3′ end of thetarget sequence (this oligonucleotide has the same polarity as the plusRNA). The present methods and buffers can also be utilized for PCR,RT-PCR, SDA and other amplification reactions known to those of skill inthe art.

The nucleic acid target to be amplified can be any selected targetsusceptible to amplification, including RNA and DNA targets. Many suchtargets are known to the skilled artisan, and they can include human,animal, viral, bacterial, parasitic and other nucleic acids. Targetnucleic acids can preferably include the nucleic acids of infectiousagents, and particularly regions of the genomes or gene products of suchinfectious agents that are useful for detecting and/or specificallyidentifying the agent. For example, one can amplify a region ofHepatitis C virus (HCV) or Human Immunodeficiency virus (HIV). Examplesof such infectious agents include bacteria such as salmonella, shigella,chlamydia, and neisseria, viruses such as hepatitis viruses,adenoviruses, human papilloma viruses, enteroviruses, and parasites suchas plasmodium. In addition, the target nucleic acid can be geneticsequences indicative of genetic disorders such as sickle cell anemia,alpha.-thalassemia, .beta.-thalassemia, and cystic fibrosis. Targetnucleic acid can also be genes associated with disease states such asinsulin-dependent diabetes or certain cancers, or nucleic acids in HLAtyping. The skilled artisan can readily adapt the present methods andbuffers to a selected nucleic acid target, given the teachings herein.

EXAMPLES

The present invention describes experiments and observations related tomodification of amplification buffer which resulted in a significantincrease in assay sensitivity. Two different methods were used; 1)heating of the TMA amplification buffer (RAR) at 37° C., 55° C., 65° C.,or 2) replacing a portion of the nucleotide triphosphates in theamplification buffer with nucleotide diphosphates. The heating methodwas shown to result in conversion of nucleotide triphosphates tonucleotide diphosphates, and thus both methods likely improvesensitivity by the same mechanism.

Example 1 HCV Assay Materials and Methods

To evaluate the effects of the buffer modifications on amplification,RAR buffer and standard VIDAS Probe D2 qHCV assay conditions asdescribed below were used, except for modifications of the RAR buffer asnoted. Target nucleic acid was Hepatitis C virus (HCV).(3′Non-translatedregion: Type I. SEQ ID NO: 5: Type II. SEQ ID NO: 6).Briefly, in vitrotranscript containing HCV (˜1 KB total) was incubated with basematrixand lysis buffer to prepare the sample. HCV target and internal controlRNA were then captured to paramagnetic particles with an oligonucleotidecomplementary to the 3′ end of HCV (primers and probes are listed inTable 1). Captured RNA was washed and then resuspended in RAR buffer(see modifications described below), which contained all of the reagentsneeded for amplification except enzymes and target (see Table 2). TheRAR-resuspended purified target was then added to VIDAS Probe strips(containing all additional reagents required for TMA amplification anddetection, such as enzymes, probes, wash solutions, and detectionsubstrate). TMA amplification was carried out in bioMerieux prototypeAmpStations (5 min. 60° C. denaturation; 70 min. 42° C. amplification),and then transferred to VIDAS instruments, which carried outsequence-specific capture of the amplicons, washing, and detection withalkaline phosphatase-conjugate probe specific for the 3′ end andfluorescent “MUP” substrate. Three sets of data were obtained fromVIDAS:

-   1) HCV detection A (Diluted sample with low SA substrate, for high    titers)-   2) HCV detection B (Undiluted sample with high SA substrate, for low    titers)-   3) IC detection (low IC=“invalid assay”).    Results are typically provided as numerical “Part A” Rates for    highly fluorescent samples, or “Part B” Rates for low fluorescence    samples.

TABLE 1 HCV Primer and Probe sequences 1259 (primer P2) (nt 17-33) (SEQID NO: 1) CCCTAGTCACGGCTAGC 1236 (primer P1 (promoter-primer) (nt 83-61)(SEQ ID NO: 2) AGGCCAGTAACGGCACTCTCTGC-T7 promoter 1246 (AKP probe) (nt32-46) (SEQ ID NO: 3) CTGTGAAAGGTCCG (methoxynucleotides; alkalinephosphatase label) 1247 (SPR probe) (nt 47-62) (SEQ ID NO: 4)TGAGCCGCATGACTGC (methoxynucleotides; AMVE) “Nt” references theposition, within the 1-98 sequences of the 3′ Non-Translated Region(HTR) of HCV, the primer/probe binds.

TABLE 2 RAR Buffer Formulation Tween 80 12.5% Tris pH 7.9 95 mM EDTA0.375 MM KCl 50 MM ZnAc 0.0765 MM MgCl 20.75 MM Glycerol   10% DMSO   5%ATP 4 MM CTP 3 MM GTP 6 MM UTP 2 MM d-ATPs 1 MM d-CTPs 1 MM d-GTPs 1 MMd-TTPs 1 MM Na Azide 0.06% P1 Primer 40 NM

Example 2 RAR Buffer Heating Results

This process consists of application of heat to RAR (also known as 1:1LAR:PRB16 mix, or 1X LAR:PRB), resulting in increased performance.Several key sets of data describe the invention, as follows.

During the course of accelerated stability testing, it was observed thatextended incubation of HCV RAR buffer at 37° C. results in a significantincrease in detected amplification product (see FIG. 1). The increasecontinues up to 48 days of incubation (final timepoint), resulting in a41-fold increase in performance.

Additional experiments demonstrated that this alteration occurs evenfaster at higher temperatures (see Table 3 and FIG. 2). Incubation at65° C. resulted in a 40-fold increase in HCV detection within 2-3 days.65° C. incubation beyond 3 days resulted in decreased performance,whereas 55° C. incubation up to 5 days (final timepoint) gave continuedincreases. It is presumed (but not known) that the decreased performancebeyond 3 days at 65° C. is due to excessive degradation of criticalassay components (perhaps nucleotide triphosphates).

TABLE 3 Days 0 1 2 3 4 5 Part A 65 C. 3.10 23.65 103.96 128.23 10.050.10 STD 1.85 16.64 60.56 56.04 4.10 0.07 % CV 60% 70% 58% 44% 41% 68%Part A 55 C. 4.25 8.26 14.75 23.48 44.96 79.99 STD 3.29 3.19 3.44 7.0337.44 41.97 % CV 77% 39% 23% 30% 83% 52%

The temperature-induced modification creates a stable alteration. 55°C.-preheated amplification reaction buffer returned to 4° C. for 3 days(longest point tested) fully maintained the higher amplificationperformance (see FIG. 3).

Example 3 HIV Assays

A beneficial effect of heat treatment (37° C.) was also noted for HIVamplification. For these experiments Liquid Amplification Reagent(“LAR”) buffer was used. The nucleotide sequences used in the HIV assaydiffered in that the target, primer and probe sequences had nosignificant similarity to HCV (except for the T7 promoter tail on the P1primer), and the composition of HIV LAR and HCV RAR are different inmany respects (such as that LAR uses HEPES instead of Tris and Tritoninstead of Tween, has no KCl or DMSO, and has significantly higher(about 2-fold) concentrations of nucleotides and Mg, and a lower pH (7.4instead of 7.9). HIV formulation and method of use are as follows:

-   -   HIV LAR [46 mM HEPES, 41.1 mM MgCl₂, 0.153 mM ZnAc, 0.25 mM        EDTA, 10.25% (v/v) glycerol, 5% (v/v) Triton-X-100, 0.095% (w/v)        NaN₃, pH 7.4, 6.0 mM each rNTP, 2.4 mM each dNTP, 50 nM T7 TMA        primer, 150 nM non-T7 TMA primer] was mixed with an equal volume        of SRB [46 mM HEPES, 40 mM KCl, 0.15 mM ZnAc, 0.25 mM EDTA,        10.25% glycerol, 0.095% NaN₃, pH7.4] to create the fmal        amplification reagent (analogous to RAR).

Half log dilutions of a 1^(e6) RNA copies/mL stock were prepared to useas standards. After target capture, the standards were amplified usingLAR buffer that had been stored in VIDAS Probe strips at 37° C. for 69days. The LAR buffer was transferred to fresh strips prior to TMAamplification. Curve results are shown in FIGS. 4-6.

Example 4 Interpretation of the Buffer Heating Results

The increased performance is likely due to improved amplification ratherthan detection. This is because Vidas Probe is an endpoint assay, andtherefore all other amplification components except the specificamplicon are removed before detection. The improved amplification islikely due to increased total amplicon yield, and/or improvedspecificity. The observation above that the alteration persists afterreturn to 4° C. (FIG. 3) suggested a chemical change has taken place.This could include the appearance of stimulatory compounds ordisappearance of inhibitory compounds. This was investigated asdescribed below.

Example 5 HPLC Analysis of Heated Amplification Mixes

The nature of the change in the buffers was investigated with HPLC

A. The 37° C.-treated HIV amplification buffer (LAR; similar but notidentical to RAR) was tested to determine what chemical changes mightexplain that increased amplification (see FIGS. 4-6). A set of eightnucleotide monophosphate (NMPs, dNMPs) as well as eight nucleotidediphosphate standards (NDPs, dNDPs) were prepared by dissolvingapproximately 2 mg samples of each of them in 4 mL of 10 mM sodiumphosphate buffer. For quantitation of these nucleotide samples by UVabsorption spectra, each of these stocks were further diluted (1:20) and100 microliter samples of the diluted solution was used for analysis bythe program that examined the individual absorbency readings at 260 nm.Based on the absorbance readings and dilution factor, an average numberof OD (absorbance units) present in the individual nucleotide sampleswas determined. For analysis on HPLC, approximately 300 microlitersamples of all the nucleotide sets containing 0.2OD were used for eachrun. Samples of HIV LAR 37° C. and HIV LAR 4° C. were used as they werereceived (1:500 dilution from the original stock). All of these sampleswere analyzed on the HPLC ion exchange column using 24 nM NaOH bufferand 375 mM perchlorate, 24 mM NaOH buffer to acquire a unique referenceprofile for each sample based on retention time.

In examining the resulting HPLC profile, several unknown peaks, four ofthem with less than four minutes retention time and two others atretention times of approximately 9.3 and 10.6 minutes appeared inaddition to the eight peaks expected and representative of the NTPspresent in the HIV LAR mixture. Upon closer examination, a third unknownpeak was visible at a retention time of approximately 6.9 minutes. Itwas observed that the unknown peaks at 9.3 minutes and 10.6 minutes inthe HIV 37° C. sample closely resembled those times obtained for dGDPand GDP, and it was also observed that a peak occurring at a retentiontime of approximately 6.9 minutes seemed to parallel the profileobtained for TDP.

In order to quantify these results, co-injections of the HIV 37° C.sample with dGDP, GDP, TDP, and UDP were performed. By looking at theareas obtained for the unknown peaks prior to injecting a nucleotidesample, it is possible to formulate a general idea of what the expectedareas of the peaks should be and then compare the known peak areas tothose obtained after injection. For example, the peak area of theunknown in the HIV 37° C. mix at a retention time of 9.3 wasapproximately 220,000. However, after injecting 2 microliters of dGDPinto 300 microliters of the HIV 37° C. mix, the peak area at theposition of the same unknown (approximately 8.95 min. for the particularrun) quadrupled to about 800,000, proving that the identity of theunknown was in fact dGDP. Again, this method led to betteridentification of the other unknown peaks present in the HIV 37° C. run.The area of the unknown peak at 10.6 minutes was about 270,000 beforeco-injecting 2 microliters of rGDP, whereas the area increased to almost600,000 after adding the rGDP. Also, the area of the unknown peak atapproximately 6.9 minutes doubled from about 105,000 to 280,923 afterinjecting 1 microliter of TDP to the HIV LAR 37° C. sample. Thus, it isconcluded that the identities of the three unknown peaks at 6.9, 9.4 and10.6 minutes in the HIV LAR 37° C. sample are dGDP, rGDP and TDP.Additionally, it was noted that the breakdown product for CTP, dCTP,ATP, dATP, the diphosphate intermediates, should have short retentiontimes and may correspond to those four peaks with retention times ofless than 4 minutes.

Overall, the most notable change detected was that the peaks identifyingnucleotide diphosphates (ATP, GTP, CTP, UTP, dATP, dGTP, dCTP, TTP)decreased and were accompanied by the appearance of peaks identified asnucleotide diphosphates. The average level of NTP loss was ˜32.5% (seeTable 4) It can be concluded that a temperature of 37° C., NTPs, anddNTPs present in the HIV LAR mixture will degrade to their diphosphateforms and some of them (dGDP, GDP, TDP) separate out as distinctivepeaks.

TABLE 4 QHIV Data NTP mM 37° C. mM 4° C. % dCTP 2.6 4.0 65% CTP 2.8 4.365% dATP 2.2 3.6 61% ATP 3.9 4.2 93% TTP 2.6 3.8 68% UTP 2.9 4.4 66%dGTP 2.2 3.6 61% GTP 2.7 4.4 61%

B. Analysis of HCV RAR buffer treated at 55° C. and 65° C. (the samesamples that showed improved performance in FIG. 2) all revealedsignificant conversion of NTPs to NDPs (see Table 5). For the three NDPproducts that were identifiable in clearly resolved peaks (ADP, GDP,dGDP), the vast majority of NTPs were converted to NDPs after 6 days at65° C. A similar rate of loss for the other NTPs suggests that theeffect occurred for all of the NTPs.

TABLE 5 HPLC analysis of heat treated RAR (HCV) A. Nucleotide DiphoshateConcentrations (mM) d- d- d- TEMP DAY CDP CDP ADP ADP TDP UDP GDP GDP55° C. 1 0.58 0.15 0.99 2 0.57 0.15 0.98 3 1.39 0.33 2.16 4 5 2.01 0.272.82 65° C. 1 1.24 0.31 2.01 2 2.12 0.52 3.54 3 2.64 0.64 4.32 4 2.810.67 4.53 5 2.83 0.67 4.53 B. Nucleotide Triphosphate Concentrations(mM) d- d- d- TEMP DAY CTP CTP ATP ATP TTP UTP GTP GTP 55° C. 0 0.923.05 1.06 3.89 0.99 1.98 0.95 6.42 1 0.74 2.42 0.84 3.27 0.79 1.58 0.745.03 2 0.72 2.40 0.82 3.22 0.79 1.57 0.74 5.02 3 0.54 1.75 0.59 2.520.58 1.17 0.50 3.39 4 5 0.41 1.32 0.44 2.13 0.45 0.90 0.40 2.67 65° C. 00.92 3.05 1.06 3.89 0.99 1.98 0.95 6.42 1 0.57 1.85 0.63 2.62 0.61 1.220.55 3.70 2 0.35 1.12 0.37 1.91 0.38 0.76 0.34 2.28 3 0.21 0.65 0.221.45 0.22 0.46 0.19 1.30 4 0.12 0.36 0.12 0.27 0.12 0.27 0.10 0.68 5 0.60.19 0.07 0.28 0.06 0.16 0.06 0.38

Example 6 Modified RAR Formulations to Mimic Heat-Induced Alteration

Since conversion of NTPs to NDPs appeared to be the most likely cause ofthe heat-induced effect, performance of an RAR buffer was examined inwhich, in the buffer, (1) NTPs were partially removed and replaced byNDP addition, (2) NTPs were partially removed, but not replaced by NDPs,and (3) NTPs were not removed but NDPs were added. Target was HCV invitro transcript as in Example 1.

We determined that replacement of 35% of the nucleotide triphosphates bynucleotide diphosphates (obtained from Sigma) resulted in a significant(>8-fold) enhancement in amplification (see FIG. 7A with Table 6A andFIG. 7B with Table 6B). In contrast, addition of diphosphates withoutcorresponding subtraction of triphosphates (i.e., resulting in a 35%increase in nucleotides) did not increase amplification (FIG. 7 andTables 6A and B). Similarly, subtraction of nucleotide triphosphates(i.e., resulting in a 35% reduction in nucleotides) did not increaseamplification (FIG. 7 and Tables 6A and B). Thus, the partialreplacement of triphosphates by diphosphates appears to be a criticalcomponent.

Note that the ˜40-fold improvement resulting from the RAR buffer heattreatments (FIG. 1, FIG. 2) is higher than that observed in the NTP/NDPreplacement experiment shown in FIG. 7 and Tables 6A and B. It is likelythat further optimization of nucleotide triphosphate/diphosphate ratioswould lead to amplification increases even greater than the 8-foldobserved, perhaps similar to or even higher than the heating results. Itis possible that NTP/NDP replacement involving only a subset ofnucleotides (e.g., replace a fraction of the GTP with GDP, withoutaltering other nucleotides) may improve performance.

TABLE 6A Trial 1: Results of Partial Replacement of NTPs with NDPs (n =8) (see also FIG. 7A) NTPs: 65% 65% 100%  100% NDPs: 35% 0   35% 0  Part A 14.09 0.54 1.31 2.64 STD 20.62 0.22 1.19 1.88 % CV 146%  41% 91% 71%

TABLE 6B Trial 2: Results of Partial Replacement of NTPs with NDPs (n =12) (see also FIG. 7B) NTPs: 100% 65% NDPs: 0   35% Part A 1.57 12.93STD 0.49 11.47 % CV  31% 89%

Throughout this application, various publications are referenced. Thedisclosures of these publications in their entireties are herebyincorporated by reference into this application in order to more fullydescribe the state of the art to which this invention pertains.

Thus, while there have been described what are presently believed to bethe preferred embodiments of the present invention, those skilled in theart will realize that other and further embodiments can be made withoutdeparting from the spirit and scope of the invention, and it is intendedto include all such further modifications and changes as come within thetrue scope of the invention.

1. A buffer for amplification of nucleic acids with nucleotidetriphosphates, comprising nucleotide triphosphates and nucleotidediphosphates of each of adenine and/or a modified nucleotide thereof,guanine and/or a modified nucleotide thereof, thymidine and/or amodified nucleotide thereof, and cytosine and/or a modified nucleotidethereof, wherein the buffer has been treated in a manner that results inthe substitution of a portion of the nucleotide triphosphates withnucleotide diphosphates, wherein the portion of the nucleotidetriphosphates substituted with nucleotide diphosphates is 35% to 60%. 2.The buffer of claim 1, wherein the buffer has been treated by heatingthe buffer to a selected temperature for a selected period of time, thetemperature and time each sufficient to increase the ratio of nucleotidediphosphates to nucleotide triphosphates in the buffer.
 3. The buffer ofclaim 1, wherein the buffer has been treated by replacing a portion ofat least one nucleotide triphosphate in the buffer with nucleotidediphosphate.
 4. A kit comprising a buffer of claim
 1. 5. A buffer foramplification of nucleic acids with nucleotide triphosphates, comprisingnucleotide triphosphates and nucleotide diphosphates of each of adenineand/or a modified nucleotide thereof, guanine and/or a modifiednucleotide thereof, thymidine and/or a modified nucleotide thereof, andcytosine and/or a modified nucleotide thereof, wherein at least onenucleotide diphosphate is present in a ratio of from 35:65 to 60:40total nucleotide diphosphate:total nucleotide triphosphate.
 6. A kitcomprising a buffer of claim
 5. 7. The buffer of claim 1, furthercomprising greater than 5% Tween
 80. 8. The buffer of claim 7,comprising greater than 10% Tween
 80. 9. A kit comprising a buffer ofclaim 7.